Hepatocellular carcinoma (HCC) is one of the most common cancers in Asia and Africa. In a previous study, HCCs from the Qidong region of China were frequently found mutated in the tumor suppressor gene p53 and in a region near TAT locus on chromosome 16. We have extended this by examining DNA from normal and tumor liver tissue obtained from over 60 patients from Qidong and Beijing. We utilized microsatellite markers specific to the long (or "q") arm of chromosome 16. Our long term goal is go identify and characterize new tumor suppressor genes on chromosome 16. Fourteen highly polymorphic microsatellite markers, mapped between 16q21 and 16q24.3, have been used in fine structure analysis of the chromosome. PCR amplification of these markers produces two bands in heterozygous alleles. If one of these is significantly reduced in the tumor sample, it indicates a potential deletion in one of the alleles. Such loss of heterozygosity (LOH) is often an indicator of a tumor suppressor gene in the deleted region. Because the tumor samples are usually contaminated with normal tissue, quantitative techniques have been developed to allow for quantitative analysis of the electrophoretograms. These techniques include separation of overlapping stutter (or shadow) bands that arise because of imperfect PCR amplification. Chromosomal disruption has been found to be extensive along the mapped region of chromosome 16. Out of 63 paired samples, only 11 (175) showed no significant LOH in any of the loci mapped. The disruption of the chromosome was very broad, with from 50 to 85% of the samples displaying detectable LOH at each of the loci. Quantitative analysis indicated two or three "hot spots" along the chromosome where the relative intensities of bands from heterozygous alleles was significantly different from that of flanking loci in an individual. This may indicate secondary "subclonal" LOH, or that the tumor tissue is polyclonal. These results indicate extensive chromosomal disruption of the "q" arm of chromosome 16, and so make it less likely that there is a new tumor suppressor gene localized near the TAT locus. However, by focusing on the above mentioned hot spots, we may be able to localize one or more small regions that might contain such tumor suppressor genes.